About micRoclean

micRoclean contains two pipelines for decontaminating low-biomass microbiome data.

For questions on installation or usage, please submit an issue or discussion via GitHub.

To run this vignette, it is suggested to download the whole “vignettes” file folder and set working directory to file location by choosing:
Session > Set working directory > To source file location

Package loading

First, we need to load the micRoclean package as well as a few others.

# required for analysis
library(micRoclean)
library(tidyverse) # %>%

# for vignette
library(knitr) # kable
library(kableExtra) # scrollbox

Data import

Next, we are going to load our count and metadata matrix. These come from a mock dilution series from Hulspusch et al. (2023) and the original data can be found here. Users can see how counts and metadata were create through the R file here.

data(pipeline1_data, package = 'micRoclean')
data(pipeline2_data, package = 'micRoclean')

# counts_1 = read.csv('counts_pipeline1.csv', row.names = 1)

counts_1 %>% kable()  %>%
  kable_styling("striped", full_width = T) %>% 
 scroll_box(width = '100%', height = "300px")